详细内容（前10条）

1. ⭐ GSE308924 从无肿瘤 C57BL/6J 小鼠淋巴结和弥漫性大 B 细胞淋巴瘤淋巴或血行性模型中肿瘤淋巴结中分选的 NK 细胞的基因表达谱。

• ✍️ 作者：未知作者
• 🏷️ 关键词：tumor、lymphoma、lymph、B cell、regex:lymph(o|atic)?
• 📝 描述：Contributors : Kamil Chahine ; Santiago F GonzálezSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe cellular components of the tumor microenvironment (TME) in non-Hodgkin B cell lymphoma demonstrate remarkable diversity. Recent evidence suggests that the spatial organization of malignant, immune and stromal cells within the TME is associated with clinical outcome and response to therapy. Yet, whether tumor cells distribution within the distinct nodal compartments, following lymphatic or hematogenous dissemination further influence the shaping of the TME and the antitumoral immune response remains unclear. We used Bulk RNA sequencing to analyze the diversity transcriptomic profiles of NK cells in 3 different conditions.
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2. ⭐ GSE318707 ST8Sia6依赖性糖基化抑制肠道炎症和致病性Th1和Th17程序

• ✍️ 作者：未知作者
• 🏷️ 关键词：inflammation、gut、regex:gut(-?microbiome)?
• 📝 描述：Contributors : Virginia S Shapiro ; Sydney B CrottsSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusSingle-cell suspensions of small bowel lamina propria, small bowel epithelium, and whole colon were purified from mice sufficient, deficient, and heterozygous for sialic acid transferase ST8Sia6. Cells were enriched for CD45 expression, hashtagged according to genotype, and analyzed by 10x scRNA sequencing using the Illumina Novaseq 6000 as well as by 10X CITEseq to identify hashtags.
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3. ⭐ GSE320403 通过空间转录组学分析揭示视黄酸受体信号在酒精相关性肝病消退过程中肝细胞中的作用

• ✍️ 作者：未知作者
• 🏷️ 关键词：spatial、spatial transcriptomics、transcriptomics
• 📝 描述：Contributors : Irina Tikhanovich ; Michael SchonfeldSeries Type : OtherOrganism : Mus musculusAbstinence is beneficial for patients with alcohol-associated liver disease (ALD), but disease resolution after alcohol cessation occurs slowly and only in a subset of patients. Mechanisms of fibrosis resolution in ALD are not yet fully understood. Previous work highlights the importance of liver niche remodeling around areas of fibrosis that involves protein and metabolite mediated cell-cell crosstalk between hepatocytes and non-parenchymal cells. We aimed to study the mechanisms of ALD resolution using spatial transcriptomics. We found that retinoic acid metabolism strongly associated with improved fibrosis resolution in a mouse model of ALD. In agreement with this finding, mice treated with RAR agonist AM580 after alcohol cessation showed improved fibrosis resolution. Spatial transcriptomics analysis of agonist treated mice and controls suggested that RAR activation dramatically altered liver niches thus promoting pro-resolving changes in liver cells.
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4. GSE308962 Eµ-myc淋巴瘤细胞在细胞培养中以及从C57BL/6J小鼠淋巴结中分选出的细胞通过淋巴或血液途径扩散后的基因表达谱。

• ✍️ 作者：未知作者
• 🏷️ 关键词：lymphoma、regex:lymph(o|atic)?
• 📝 描述：Contributors : Kamil Chahine ; Santiago F GonzálezSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe cellular components of the tumor microenvironment (TME) in non-Hodgkin B cell lymphoma demonstrate remarkable diversity. Recent evidence suggests that the spatial organization of malignant, immune and stromal cells within the TME is associated with clinical outcome and response to therapy. Yet, whether tumor cells distribution within the distinct nodal compartments, following lymphatic or hematogenous dissemination further influence the shaping of the TME and the antitumoral immune response remains unclear. We used Bulk RNA sequencing to analyze the diversity transcriptomic profiles of Eµ-myc lymphoma in 3 different conditions.
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5. GSE316123 利用组织样本进行低投入量全基因组lncRNA-染色质相互作用的微流控技术

• ✍️ 作者：未知作者
• 🏷️ 关键词：genome
• 📝 描述：Contributors : Jenna A Catalano ; Chang LuSeries Type : OtherOrganism : Homo sapiens ; Mus musculusLong noncoding RNAs (lncRNAs) regulate gene expression through binding to DNA, various RNAs, and proteins, playing potentially important but poorly understood roles in development and diseases. Existing approaches for profiling lncRNA–chromatin interactions at the genome scale require large quantities of input material (e.g., 100 million cells per assay). Applying these technologies to tissue samples has been challenging especially when examination of a specific cell type is desired. Here we demonstrate a low-input microfluidic technology based on Chromatin Isolation by RNA purification (ChIRP) process for mapping lncRNA–chromatin interactions using as few as 50,000 cells. We validate our technology on two lncRNAs of different sizes in human and mouse cell lines and brain tissue. We apply our technology muChIRP-seq to neuronal nuclei from postmortem human brain tissues and integrate our data with histone and RNA-seq data to understand the role of lncRNA in the epigenomic and transcriptomic landscape of schizophrenia. MuChIRP-seq enables the mapping of lncRNA–chromatin interactions in tissue samples and in a cell-type-specific fashion, unlocking new opportunities to study lncRNA-mediated gene regulations.
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6. GSE293582 Retinoic acid drives cell fate specification, maturation and retinal regionality in human retinal organoids [Visium]

• ✍️ 作者：未知作者
• 🏷️ 关键词：Visium
• 📝 描述：Contributors : Benjamin Y Lim ; Carissa Chen ; Anna Fredericks ; Elham Nilli ; Santiago M Mora ; Megan Weatherstone ; To Ha Loi ; Peter Newman ; Nader Arymanesh ; Hala Zreiqat ; Patrick Tam ; Pengyi Yang ; Anai Gonzalez-CorderoSeries Type : OtherOrganism : Homo sapiensRetinoic acid (RA) is a key morphogen in human retinal development, activating transcriptional programs that drive retinal progenitor differentiation and photoreceptor development, ensuring proper spatial organisation within the neural retina, essential for vision. Despite its well-established role in retinal patterning, the concentration-dependent effects of RA on human retinal cell fate specification and the regional definition of the primate macula and peripheral retina remain poorly understood. Here, we show that temporal and dosage-dependant modulation of RA during human retinal organoid differentiation induces distinct changes in retinal cell abundance, maturation, and organisation. Single-cell transcriptomics and protein analysis revealed that RA dosage influenced the relative abundance and maturation of photoreceptors and retinal interneurons. Spatial transcriptomics analyses demonstrated that low RA levels biased retinal organoids toward a macular-like regional identity, whereas high RA levels promoted peripheral-like development. Collectively, our findings emphasise the critical role of RA signalling in retinal maturation and regional specification. This study elucidates mechanisms involved in human retinal development and we anticipate that controlled RA modulation in retinal organoids provides a strategy to refine disease modelling of inherited retinal disorders and enhance the specific generation of photoreceptors suitable for transplantation and regenerative therapies.
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7. GSE293457 视黄酸驱动人类视网膜类器官的细胞命运决定、成熟和视网膜区域性[scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：scRNA
• 📝 描述：Contributors : Benjamin Y Lim ; Carissa Chen ; Anna Fredericks ; Elham Nilli ; Santiago M Mora ; Megan Weatherstone ; To Ha Loi ; Peter Newman ; Nader Arymanesh ; Hala Zreiqat ; Patrick Tam ; Pengyi Yang ; Anai Gonzalez-CorderoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRetinoic acid (RA) is a key morphogen in human retinal development, activating transcriptional programs that drive retinal progenitor differentiation and photoreceptor development, ensuring proper spatial organisation within the neural retina, essential for vision. Despite its well-established role in retinal patterning, the concentration-dependent effects of RA on human retinal cell fate specification and the regional definition of the primate macula and peripheral retina remain poorly understood. Here, we show that temporal and dosage-dependant modulation of RA during human retinal organoid differentiation induces distinct changes in retinal cell abundance, maturation, and organisation. Single-cell transcriptomics and protein analysis revealed that RA dosage influenced the relative abundance and maturation of photoreceptors and retinal interneurons. Spatial transcriptomics analyses demonstrated that low RA levels biased retinal organoids toward a macular-like regional identity, whereas high RA levels promoted peripheral-like development. Collectively, our findings emphasise the critical role of RA signalling in retinal maturation and regional specification. This study elucidates mechanisms involved in human retinal development and we anticipate that controlled RA modulation in retinal organoids provides a strategy to refine disease modelling of inherited retinal disorders and enhance the specific generation of photoreceptors suitable for transplantation and regenerative therapies.
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8. GSE325293 HIF-1α 和 HIF-2α 转录因子差异性地调节肺泡巨噬细胞功能

• ✍️ 作者：未知作者
• 🏷️ 关键词：macrophage
• 📝 描述：Contributors : Elena Priego ; Irene Adan-Barrientos ; Ruth Conde-Garrosa ; Sarai Martínez-Cano ; Iria Sánchez ; Diego Mañanes ; Annalaura Mastrangelo ; Joaquín Amores ; Helena M Izquierdo ; David SanchoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAlveolar Macrophages (AMs) reside in the alveoli, therefore maintaining an active degradation of hypoxia-inducible transcription factors (HIF) mediated by Von Hippel-Lindau protein (pVHL). We previously found that Vhl-deficient AMs are immature and functionally impaired. Here we investigated the specific contribution of HIF-1α and HIF-2α isoforms to the regulation of the AM function. Our work demonstrates that in Vhl-deficient macrophages, both HIF-1α and HIF-2α contribute to AM defective self-renewal, while HIF-2α plays a central role in regulating the impaired AM maturation associated with pVHL loss. HIF-1α promotes a glycolytic shift in alveolar macrophages, while HIF-2α hinders lipid oxidation and surfactant clearance. Thus, HIF-2α raises as a selective critical factor restraining the therapeutic potential of AMs to degrade surfactant excess in mice that have developed pulmonary alveolar proteinosis (PAP). Overall, regulation of both HIF-1α and HIF-2α isoforms is required for an optimal AM function.
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9. GSE325226 CD69 调控表观遗传印记记忆 CD4+ T 细胞的组织动态 [scRNA-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：scRNA
• 📝 描述：Contributors : Rui Hirasawa ; Chiaki Iwamura ; Masahiro Kiuchi ; Hiroyuki Yagyu ; Takahisa Hishiya ; Norie Hamaguchi ; Atsushi Sasaki ; Kohei Kakinuma ; Kanae Ohishi ; Akane Kurosugi ; Masahiro Nemoto ; Kota Kokubo ; Takuto Hiramoto ; Tomohisa Iinuma ; Syuji Yonekura ; Atsushi Onodera ; Motoko Y Kimura ; Shinichiro Motohashi ; Damon J Tumes ; Toyoyuki Hanazawa ; Toshinori Nakayama ; Seiji Ohtori ; Kiyoshi HiraharaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTissue-resident memory T (TRM) cells reside in non-lymphoid tissues and provide the first line of defense against pathogens. A subset of TRM cells can egress from non-lymphoid tissues into the circulation. However, the functional consequences and the extent of epigenetic imprinting in recirculating TRM cells remain unknown. We herein demonstrate that in CD4+ TRM cells, the CD69-S1PR1 axis controls tissue residency, and that interrupting this axis results in ablation of lung CD4+ TRM cells. A subpopulation of CD69+CD4+ TRM cells re-entered circulation via lymphatic vessels, where they epigenetically maintained the characteristics of TRM cells in both mice and humans. Circulating Ex-lung-TRM cells in mice caused enhanced skin inflammation compared to circulating memory cells. Furthermore, we identified GPR183 and CD161 as potential markers of Ex-TRM in human PBMC. In chronic inflammatory diseases, the transposition of allergic inflammation to multiple tissues may therefore occur via recirculation of tissue-imprinted memory CD4+ T cells.
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10. GSE325225 CD69 调控表观遗传印记记忆 CD4+ T 细胞的组织动态 [scATAC-seq]

• ✍️ 作者：未知作者
• 🏷️ 关键词：scATAC
• 📝 描述：Contributors : Rui Hirasawa ; Chiaki Iwamura ; Masahiro Kiuchi ; Hiroyuki Yagyu ; Takahisa Hishiya ; Norie Hamaguchi ; Atsushi Sasaki ; Kohei Kakinuma ; Kanae Ohishi ; Akane Kurosugi ; Masahiro Nemoto ; Kota Kokubo ; Takuto Hiramoto ; Tomohisa Iinuma ; Syuji Yonekura ; Atsushi Onodera ; Motoko Y Kimura ; Shinichiro Motohashi ; Damon J Tumes ; Toyoyuki Hanazawa ; Toshinori Nakayama ; Seiji Ohtori ; Kiyoshi HiraharaSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTissue-resident memory T (TRM) cells reside in non-lymphoid tissues and provide the first line of defense against pathogens. A subset of TRM cells can egress from non-lymphoid tissues into the circulation. However, the functional consequences and the extent of epigenetic imprinting in recirculating TRM cells remain unknown. We herein demonstrate that in CD4+ TRM cells, the CD69-S1PR1 axis controls tissue residency, and that interrupting this axis results in ablation of lung CD4+ TRM cells. A subpopulation of CD69+CD4+ TRM cells re-entered circulation via lymphatic vessels, where they epigenetically maintained the characteristics of TRM cells in both mice and humans. Circulating Ex-lung-TRM cells in mice caused enhanced skin inflammation compared to circulating memory cells. Furthermore, we identified GPR183 and CD161 as potential markers of Ex-TRM in human PBMC. In chronic inflammatory diseases, the transposition of allergic inflammation to multiple tissues may therefore occur via recirculation of tissue-imprinted memory CD4+ T cells.
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1. 一种前景可观的脂肪肝治疗方法可能会增加患癌风险。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：A surprising new study reveals that blocking a supposedly protective enzyme, Caspase-2, could actually backfire—raising the risk of chronic liver damage and cancer over time. Researchers found that without this enzyme, liver cells grow abnormally large and accumulate genetic damage, leading to inflammation, scarring, and eventually tumors, especially with age. While inhibiting Caspase-2 may offer short-term benefits, such as reducing fatty liver disease, the long-term consequences appear dangerous.
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2. 新的血液检测方法有望在胰腺癌发展到晚期之前将其发现。

• ✍️ 作者：未知作者
• 🏷️ 关键词：cancer
• 📝 描述：A new blood test could change the outlook for one of the deadliest cancers—pancreatic cancer—by catching it much earlier than ever before. Researchers identified two previously unknown proteins in the blood that, when combined with existing markers, dramatically improved detection accuracy. The four-marker test was able to spot pancreatic cancer in over 90% of cases and performed especially well even in early stages, when treatment has the best chance of success.
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3. 科学家在大脑中发现阿尔茨海默病隐藏的“死亡开关”

• ✍️ 作者：未知作者
• 🏷️ 关键词：Alzheimer
• 📝 描述：Scientists have uncovered a hidden “death switch” in the brain that may be driving Alzheimer’s disease—and even found a way to turn it off in mice. The culprit is a toxic pairing of two proteins that, when combined, triggers the destruction of brain cells and fuels memory loss. By using a new compound to break apart this deadly duo, researchers were able to slow disease progression, protect brain cells, and even reduce hallmark amyloid buildup.
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• GSE316968 棕榈酸酯处理对庞贝病患者成纤维细胞转录组的影响
• GSE313818 RNF25 通过抑制整合应激反应的激活来赋予对氮杂胞苷诱导的 mRNA 损伤的耐受性 [RNA-seq]
• GSE309676 转移性骨肉瘤非肿瘤肺、肝、肾转录组的综合分析
• GSE294175 HER2 过表达驱动耐药持续患者接受一线 Amivantamab 和 Lazertinib 治疗 EGFR 突变型非小细胞肺癌
• GSE264056 VLA-4激动剂促进同种异体造血干细胞的植入和细胞免疫重建
• GSE262305 硼替佐米通过增强肺腺癌中 STING 和 IFN-γ 信号通路提高免疫疗法的疗效
• GSE310900：接受新辅助治疗的患者的FFPE原发性Her2阳性乳腺癌样本的基因表达谱
• GSE295612 APOE4 表达对雄性和雌性小鼠的脑膜免疫、脑脂质组成和认知能力产生不同的影响